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Notes on application for codon usage / composition bias

  Correspondence on new application for showing codon
usage tables:

> You can look in the file
.../share/EMBOSS/acd/embossdata.acd :
> selection: reject [
> default: "3, 5, 6"
> minimum: "1"
> maximum: "6"
> values: "None, AAINDEX, CVS, CODONS, PRINTS,
> delimiter: ","
> header: "Directories to ignore"
> information: "Select directories"
> help: "This specifies the names of the
sub-directories of the
> EMBOSS data directory that should be
ignored when
> displaying data
> directories."
> button: "Y"
> ]
> So, by default CVS, PRINTS and PROSITE are rejected.

Yes, that makes sense now !

> This does not work, there is no way to reject the
files in
> the base data directory. The best you can do is to
add on the
> command line
> -reject=2,3,5,6,7 or -reject=
however is :

Yeah, that is of course the most obvious ;-) Thing is
that I wanted to
do it in an emboss-only way so that it would be
possible to run the
emboss command via a soaplab service. The latter should
provide a means
to dynamically fetch a list of codon usage tables. More
or less like
showdb is doing.
> Hope this helps,

We are looking at ways to do that ... can be tricky if
cutgextract has
been run. Any suggestions? A showdata application perhaps?

Hope that helps,


Yes that could be a start. You could give the directory
name as a
parameter, the oposite of the -reject parameter
(-include ?).
In it's basic form it can just list the file content
like embossdata
-showall is doing.
An example command that lists all the codon tables
could be: 'showdata
-include CODONS'.